Variant report

Variant	rs1992753
Chromosome Location	chr2:179145455-179145456
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr2:179144942-179145505	HCT-116	colon:	n/a	n/a
2	RAD21	chr2:179144826-179145478	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr2:179145448-179145518	GM10266	blood:	n/a	n/a
4	SMC3	chr2:179144925-179145511	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr2:179144909-179145525	HCT-116	colon:	n/a	chr2:179145190-179145199
6	CTCF	chr2:179144894-179145546	A549	lung:	n/a	chr2:179145190-179145199
7	RAD21	chr2:179145027-179145486	GM12878	blood:	n/a	n/a
8	RAD21	chr2:179144957-179145467	MCF-7	breast:	n/a	n/a
9	CTCF	chr2:179144905-179145459	SK-N-SH	brain:	n/a	chr2:179145190-179145199
10	CTCF	chr2:179144933-179145461	HCT-116	colon:	n/a	chr2:179145190-179145199
11	RAD21	chr2:179144899-179145455	HCT-116	colon:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:179140423..179143363-chr2:179145106..179148015,2	K562	blood:
2	chr2:178848052..178848705-chr2:179144772..179145465,2	K562	blood:
3	chr2:179058189..179060134-chr2:179145387..179147817,2	MCF-7	breast:

Variant related genes	Relation type
OSBPL6	TF binding region
ENSG00000079156	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10167889	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12467696	1.00[EUR][1000 genomes]
rs12471986	0.86[EUR][1000 genomes]
rs4893850	0.81[EUR][1000 genomes]
rs4894005	0.86[EUR][1000 genomes]
rs4894006	0.99[EUR][1000 genomes]
rs62176069	0.87[EUR][1000 genomes]
rs62176070	0.87[EUR][1000 genomes]
rs62176071	0.83[EUR][1000 genomes]
rs62176072	0.83[EUR][1000 genomes]
rs62176076	0.81[EUR][1000 genomes]
rs62176078	0.81[EUR][1000 genomes]
rs62177255	0.82[EUR][1000 genomes]
rs62177256	0.98[EUR][1000 genomes]
rs62177257	1.00[EUR][1000 genomes]
rs62179160	0.86[EUR][1000 genomes]
rs62179161	0.86[EUR][1000 genomes]
rs62179162	0.97[EUR][1000 genomes]
rs62179163	0.99[EUR][1000 genomes]
rs62179164	0.99[EUR][1000 genomes]
rs62179165	0.86[EUR][1000 genomes]
rs62179167	0.97[EUR][1000 genomes]
rs6433718	0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs6743122	0.86[EUR][1000 genomes]
rs73032523	0.83[EUR][1000 genomes]
rs7349264	0.87[EUR][1000 genomes]
rs7559125	0.83[EUR][1000 genomes]
rs7559527	0.83[EUR][1000 genomes]
rs7570485	0.83[EUR][1000 genomes]
rs7599195	0.81[EUR][1000 genomes]
rs9808049	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009312	chr2:178924318-179215566	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv536057	chr2:178924318-179215566	Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv875452	chr2:178963445-179167766	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1011423	chr2:179084407-179166160	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv834466	chr2:179140792-179284778	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1992753	HOXD4	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179133800-179146800	Weak transcription	Esophagus	oesophagus
2	chr2:179136800-179146800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr2:179141000-179146800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:179141200-179146800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:179141600-179145600	Enhancers	Fetal Intestine Small	intestine
6	chr2:179142800-179146600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr2:179142800-179146800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:179142800-179146800	Weak transcription	Brain Angular Gyrus	brain
9	chr2:179143000-179146600	Weak transcription	A549	lung
10	chr2:179143000-179146800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr2:179143000-179146800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:179143000-179146800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:179143000-179160200	Weak transcription	Fetal Kidney	kidney
14	chr2:179143200-179160800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:179143200-179188600	Weak transcription	Brain Anterior Caudate	brain
16	chr2:179143400-179146800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:179143600-179146600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr2:179144000-179146800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr2:179144000-179148400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:179144200-179163800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:179144400-179146800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:179144400-179153000	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr2:179144400-179154600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:179144600-179146600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:179144600-179146600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr2:179144600-179146600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr2:179144600-179146600	Weak transcription	Hela-S3	cervix
28	chr2:179144600-179146600	Weak transcription	K562	blood
29	chr2:179144600-179146600	Weak transcription	Osteobl	bone
30	chr2:179144600-179146800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:179144600-179146800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr2:179144600-179146800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:179144600-179146800	Weak transcription	Psoas Muscle	Psoas
34	chr2:179144600-179147000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:179144600-179147000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr2:179144600-179149400	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:179144600-179149600	Weak transcription	HSMMtube	muscle
38	chr2:179144600-179155000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:179144800-179146600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr2:179144800-179146600	Weak transcription	NHEK	skin
41	chr2:179145000-179146600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:179145000-179146600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:179145000-179146600	Weak transcription	NH-A	brain
44	chr2:179145000-179146800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr2:179145000-179159200	Weak transcription	Liver	Liver
46	chr2:179145200-179146400	Weak transcription	Fetal Intestine Large	intestine
47	chr2:179145200-179146600	Weak transcription	HUVEC	blood vessel
48	chr2:179145400-179146600	Weak transcription	HMEC	breast

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